Confusingly, the rightful ruler of Dinohattan is King Bowser (Lance Henrikson), a righteous and reasonable monarch who was turned into a giant sentient fungus by King Koopa. It seems very strange to name one of the movie’s heroes after the usual series antagonist, but this decision was reportedly made during a series of extensive on-set script rewrites. At earlier points of production, the King had a number of different names and Bowser is only confirmed through the movie’s novelization and screenplay; his name is never mentioned on-screen.
At the end of the movie, however, he is restored to his normal human form, allowing him to retake his throne and return Dinohattan to its former glory. This is another reference to “Super Mario Bros. 3” In that game, players move from land to land of a sprawling kingdom defeating a series of Koopalings, each of whom are revealed to be a king transformed by Bowser.
Once the Koopalings are defeated, the kings re-assume their human forms and take their rightful place on the throne, just like King Bowser does in the movie. As a matter of fact, monsters who end up transforming into humans pop up a lot in this franchise, as even Mario’s earlier animated movie featured a similar scene in its conclusion.